BN1812 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 3.8807e-05 1.4299e-03
Layer 2 9.7943e-05 1.2783e-02
WM 1.1660e-04 2.5560e-01
Layer 5 3.4023e-04 1.9318e-03
Layer 4 9.8476e-04 3.0618e-03
Layer 6 2.7405e-03 2.3530e-02
Layer 1 1.5709e-01 2.6575e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.3027 0.6815
NDRG4 Layer 5 2.2803 0.6172
ATP6V0C Layer 5 2.1016 0.6171
SLC17A7 Layer 5 2.1680 0.6100
TPI1 Layer 5 2.2598 0.6063
SH3GL2 Layer 5 2.1973 0.6052
TUBB4B Layer 4 2.2754 0.6048
EEF1A2 Layer 5 2.3086 0.6041
USP22 Layer 3 2.4121 0.6030
TUBB Layer 5 2.2393 0.6023
SYP Layer 3 2.4883 0.6021
RAB6A Layer 5 2.0957 0.6016
PLD3 Layer 3 2.2070 0.6011
SYN2 Layer 4 2.2676 0.5996
ARPP19 Layer 3 2.1621 0.5990
NSF Layer 3 2.3867 0.5983
ATP1A1 Layer 3 2.2227 0.5967
SNCG Layer 4 2.5479 0.5966
UBA1 Layer 3 2.0859 0.5962
TTC9B Layer 4 2.8555 0.5961
GAP43 Layer 3 2.3867 0.5960
MAGED1 Layer 5 2.2617 0.5948
ATP6V1E1 Layer 4 2.2871 0.5927
GDI1 Layer 5 2.0820 0.5924
CLSTN1 Layer 5 2.0449 0.5922
NGRN Layer 3 2.1719 0.5909
PRKAR1B Layer 3 2.3809 0.5908
NDUFB4 Layer 5 2.0625 0.5906
GUCY1B1 Layer 3 2.3281 0.5905
TUBB3 Layer 5 2.1035 0.5899
PHYHIP Layer 3 2.2832 0.5887
RPL15 Layer 5 2.0488 0.5885
ATP6V1B2 Layer 3 2.1680 0.5884
MORF4L1 Layer 5 2.1318 0.5881
PGRMC1 Layer 3 2.1387 0.5875
RAB3A Layer 3 2.2324 0.5868
ATP5IF1 Layer 3 2.4297 0.5863
STMN1 Layer 4 2.0654 0.5860
EIF4G2 Layer 5 2.2490 0.5858
ARL6IP1 Layer 5 2.2832 0.5850
GABRA1 Layer 3 2.2676 0.5840
RGS4 Layer 3 2.4121 0.5839
BEX2 Layer 5 2.1152 0.5839
SERPINI1 Layer 3 2.4180 0.5833
GPX4 Layer 3 2.1914 0.5830
STXBP1 Layer 3 2.2324 0.5824
NDUFA5 Layer 5 2.2881 0.5824
YWHAG Layer 5 2.1387 0.5819
APP Layer 3 2.2168 0.5807
MTCH1 Layer 3 2.1191 0.5801

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1812
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1812_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1812/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1812/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1812/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1812/report/PD/BN1812_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1812/report/PD/BN1812_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:34:41
  • Number of Processes: 10
  • Spending Time: 0h 2m